Convert gene symbols to Ensembl IDs

Usage

gene2ensembl(x, ref = NULL, species = c("human", "mouse"))

Arguments

x: Character vector of gene symbols.
ref: Data frame with columns symbol and ensembl_id. If NULL (default), a full reference is downloaded via download_gene_ref — this may trigger a network request. For examples and tests, pass toy_gene_ref() instead.
species: One of "human" or "mouse". Controls symbol case normalization before matching. Default: "human".

Value

A data.frame with columns symbol (original input), symbol_std (case-normalized), and ensembl_id. Unmatched entries have NA in ensembl_id. If the reference contains duplicated normalized symbols, the first match is used with a warning.

Examples

ref <- toy_gene_ref(species = "human")
gene2ensembl(c("tp53", "brca1", "MYC"), ref = ref, species = "human")
#>   symbol symbol_std      ensembl_id
#> 1   tp53       TP53 ENSG00000141510
#> 2  brca1      BRCA1 ENSG00000012048
#> 3    MYC        MYC ENSG00000136997

ref <- toy_gene_ref(species = "mouse")
gene2ensembl(c("Zbp1", "Sftpd"), ref = ref, species = "mouse")
#>   symbol symbol_std ensembl_id
#> 1   Zbp1       zbp1       <NA>
#> 2  Sftpd      sftpd       <NA>